Multi-Channel Nanopore Sensing By Local Electrical Potential Measurement

ABSTRACT

There is provided a multi-channel nanopore sensor having a plurality of independent nanopore sensors. Each independent nanopore sensor includes a nanopore disposed in a support structure. A fluidic connection is between a first fluidic reservoir, common to all of the independent nanopore sensors, and an inlet to the nanopore, with a first ionic solution of a first ionic concentration disposed in the first fluidic reservoir. A fluidic connection is between a second fluidic reservoir, common to all of the independent nanopore sensors, and an outlet from the nanopore, with a second ionic solution of a second ionic concentration, different than the first ionic concentration, disposed in the second fluidic reservoir. An electrical transduction element, disposed in contact with that ionic solution having a lower ionic concentration, is arranged at a site that produces an electrical signal indicative of electrical potential local to that ionic solution having a lower ionic concentration.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of copending application Ser. No.15/616,225, filed Jun. 7, 2017, which is a continuation of applicationSer. No. 14/009,348, filed Oct. 2, 2013, now issued as U.S. Pat. No.9,702,849, which is the National Stage of International Application No.PCT/US11/034426, filed Apr. 29, 2011, which claims the benefit of U.S.Provisional Application No. 61/471,345, filed Apr. 4, 2011, the entiretyof all which is hereby incorporated by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under Contract No.5DP1OD003900 awarded by the National Institute of Health. The Governmenthas certain rights in the invention.

BACKGROUND

This invention relates generally to sensing systems that employ ananopore sensor, and more particularly relates to techniques for sensingspecies as the species translocate through a nanopore sensor.

Solid state and biological nanopores are increasingly the focus ofconsiderable effort towards the development of a low cost, highthroughput sensing system that can be employed for sensing a wide rangeof species, including single molecules. For example, there is has beenproposed the use of solid state nanopores for enabling single-moleculeDNA sequencing technology. While single DNA bases produced by enzymaticcleavage of DNA have been detected and differentiated using modifiedprotein nanopores, the goal of sequencing a single-stranded DNA (ssDNA)molecule by translocation of the molecule through a nanopore has not yetbeen fully realized.

One proposed approach for nanopore sensing is based on a method in whichthere is detected a modulation of ionic current passing through ananopore that is disposed in a membrane or other support structure.Given a molecule that is provided in an ionic solution to betranslocated through a nanopore, as the molecule translocates throughthe nanopore, the ionic current that passes through the nanopore iscorrespondingly decreased from the ionic current passing through thenanopore without a molecule. This nanopore sensing approach is limitedin that it is in general quite difficult to record the small picoampereionic current signals that are characteristic of molecular nanoporetranslocation at a bandwidth that is consistent with very fast moleculartranslocation speeds. The speed of a DNA molecule translocation througha nanopore can be ˜1 μs/nucleotide. Furthermore, the recording of suchsmall current signals at high bandwidth in a parallel multiplexed formathas been shown to be extremely difficult.

To circumvent the technical challenges of the ionic current measurementmethod for nanopore sensing, several alternative nanopore sensingmethods have been proposed. Such alternative methods can be generalizedas directed to an effort to record larger and relatively more-localnanopore signals employing electronic sensors that are integrated withthe nanopore. These nanopore sensing methods include, e.g., measurementof capacitive coupling across a nanopore and tunnelling currentmeasurements through a species translocating a nanopore. While providinginteresting alternative sensing techniques, such capacitive coupling andtunnelling current measurement techniques have not yet improved upon theconventional ionic current detection technique for nanopore sensing, andionic current detection techniques remain challenged by signal amplitudeand signal bandwidth issues.

SUMMARY OF THE INVENTION

There is provided a multi-channel nanopore sensor that overcomes themeasurement sensitivity and signal bandwidth limitations of conventionalnanopore sensors and nanopore sensing techniques by employing amulti-channel structure that enables local electrical potential sensing.The multi-channel nanopore sensor includes a plurality of independentnanopore sensors. Each independent nanopore sensor in the plurality ofindependent nanopore sensors includes a nanopore disposed in a supportstructure. A fluidic connection is disposed between a first fluidicreservoir, common to all of the independent nanopore sensors, and aninlet to the nanopore, with a first ionic solution of a first ionicconcentration disposed in the first fluidic reservoir. A fluidicconnection is disposed likewise between a second fluidic reservoir,common to all of the independent nanopore sensors, and an outlet fromthe nanopore, with a second ionic solution of a second ionicconcentration, different than the first ionic concentration, disposed inthe second fluidic reservoir. Each independent nanopore sensor includesan electrical transduction element that is disposed in contact with thationic solution, of the first and second ionic solutions, which has alower ionic concentration, having a lower ionic concentration. Theelectrical transduction element is arranged at a site that produces inthe electrical transduction element an electrical signal indicative ofelectrical potential local to that ionic solution having a lower ionicconcentration.

This multi-channel nanopore sensor arrangement enables local electricalpotential sensing with high sensitivity, high bandwidth, and largesignal differentiation between differing objects translocating througheach nanopore in the plurality of independent nanopore sensors. Eachindependent nanopore sensor operates independently even with integrationinto a single multi-channel nanopore sensor. As a result, high-throughput nanopore sensing applications, such as DNA sequencing, can beaccomplished both efficiently and precisely with the multi-channelnanopore sensor. Other features and advantages will be apparent from thefollowing description and accompanying figures, and from the claims

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A is a schematic circuit diagram of a first example nanoporesensor configuration for measuring local electrical potential;

FIG. 1B is a circuit diagram of an example transistor implementation ofthe nanopore sensor configuration of FIG. 1A;

FIG. 1C is a schematic circuit diagram of a second example nanoporesensor configuration for measuring a local electrical potential;

FIG. 1D is circuit diagram of an example transistor implementation ofthe nanopore sensor configuration of FIG. 1C;

FIG. 1E is a circuit diagram of an example transistor implementation ofa combination of the sensor configurations of FIGS. 1A and 1C;

FIG. 1F is a schematic plan view of a single electron transistorimplementation of a nanopore sensor configuration for measuring localelectrical potential;

FIG. 1G is a schematic plan view of a quantum point contactimplementation of a nanopore sensor configuration for measuring localelectrical potential;

FIG. 1H is a schematic side view of a lipid bilayer includingfluorescent dye arranged for implementation of a protein nanopore sensorconfiguration for measuring local electrical potential;

FIG. 2A is a schematic diagram and corresponding circuit elements for ananopore sensor configuration for measuring local electrical potential;

FIG. 2B is a circuit diagram for the nanopore sensor transistorimplementation of FIG. 1B;

FIG. 3A is a schematic side view of the geometric features of a nanoporesensor configuration for measuring local electrical potential as-definedfor quantitative analysis of the sensor;

FIGS. 3B-3C are plots of the electrical potential in a nanopore of ananopore sensor for measuring local electrical potential, here plottedas a function of distance from the nanopore into the cis reservoir, fora configuration in which the cis and trans reservoirs include fluidicsolutions of equal ionic concentration and for a configuration in whichthe cis and trans reservoirs include fluidic solutions of unequal ionicconcentration, respectively;

FIGS. 3D-3E are plots of the electrical field in a nanopore of ananopore sensor for measuring local electrical potential, correspondingto the plots of electrical potential of FIGS. 3B-3C, respectively;

FIG. 4A is a plot of the change in potential in a nanopore for a 50nm-thick nanopore membrane and a configuration of a 1 V transmembranevoltage (TMV) for electrophoretic species translocation as a dsDNAmolecule translocates through the nanopore, as a function of theC_(Cis)/C_(Trans) ionic concentration ratio for various nanoporediameters below 10 nm where the nanopore is configured for localelectrical potential measurement;

FIG. 4B is a plot of the change in potential in the trans reservoir fora 10 nm-diameter nanopore at 1 V TMV for the conditions of the plot ofFIG. 4A;

FIG. 4C is a plot of noise sources and signal as a function of recordingbandwidth for a nanopore sensor configured for local electricalpotential measurement;

FIG. 4D is a plot of the bandwidth of a nanopore sensor configured forlocal electrical potential measurement as a function of cis chambersolution concentration for a range of reservoir solution concentrationratios;

FIG. 4E is a plot of signal decal length from the nanopore site in ananopore configured for local electrical potential measurement as afunction of cis and trans reservoir solution concentration ratio;

FIG. 5 is a schematic view of a nanopore sensor configured for localelectrical potential measurement with a nanowire FET disposed on amembrane;

FIG. 6 is a perspective view of one example implementation of thenanopore sensor configuration of FIG. 5;

FIGS. 7A-7B are a schematic view of a nanopore sensor configured forlocal electrical potential measurement with a nanowire FET disposed on agraphene membrane, and a plan view of an example implementation of thisnanopore sensor, respectively;

FIGS. 8A-8B are a schematic view of a nanopore sensor configured forlocal electrical potential measurement with a graphene layer disposed ona nanowire FET, and a plan view of an example implementation of thisnanopore sensor, respectively;

FIGS. 9A-9B are a schematic view of a nanopore sensor configured forlocal electrical potential measurement with a graphene membrane, and aplan view of an example implementation of this nanopore sensor,respectively;

FIGS. 10A-10D are schematic plan views of example locations of ananopore with respect to a nanowire in a nanopore sensor configured forlocal electrical potential measurement;

FIG. 11 is a plot of the electrical potential signal measured for eachof the four DNA bases as a function of nanopore diameter for a nanoporesensor configured for local electrical potential measurement as the DNAbases translocate through the nanopore;

FIG. 12 is a plot of the sensitivity of a nanowire in a nanopore sensorconfigured for local electrical potential measurement before and afterformation of a nanopore at the nanowire location;

FIG. 13 A is a plot of i) measured ionic current through a nanopore andii) measured nanowire FET conductance, respectively, as DNA translocatesthrough a nanopore in a nanopore sensor configured for local electricalpotential measurement, for a TMV of 2 V and 100:1 cis/trans reservoirsolution concentration ratio, with a local potential measurement made inthe trans reservoir;

FIG. 13B is a plot of i) measured ionic current through a nanopore andii) measured nanowire FET conductance, respectively, as DNA translocatesthrough a nanopore in a nanopore sensor configured for local electricalpotential measurement, for a TMV of 2.4 V and 100:1 cis/trans reservoirsolution concentration ratio, with a local potential measurement made inthe trans reservoir;

FIG. 13C is a plot of i)measured ionic current through a nanopore andii) measured nanowire FET conductance, respectively, as DNA translocatesthrough a nanopore in a nanopore sensor configured for local electricalpotential measurement, for a TMV of 0.6 V and 1:1 cis/trans reservoirsolution concentration ratio, with a local potential measurement made inthe trans reservoir; and

FIG. 14 is a plot of i) total ionic current measured through threenanopores sharing reservoirs, ii) measured nanowire FET conductancethrough the first of the nanopores, ii) measured nanowire FETconductance through the second of the nanopores, and ii) measurednanowire FET conductance through the third of the nanopores,respectively, as DNA translocates through the nanopores in the threesensors in a nanopore sensor configured for local electrical potentialmeasurement.

DETAILED DESCRIPTION

FIGS. 1A-1E are schematic views of example nanopore sensorconfigurations that enable a local electrical potential sensing methodfor nanopore sensing. For clarity of discussion, device featuresillustrated in the figures are not shown to scale. Referring to FIG. 1A,there is shown a nanopore sensor 3 including a support structure, suchas a membrane 14, in which is disposed a nanopore 12. The nanopore 12 isconfigured in the support structure between two fluidic reservoirs shownhere schematically as a trans reservoir and a cis reservoir such thatthe nanopore 12 is the only path of fluidic communication between thecis and trans reservoirs. One reservoir is connected to an inlet to thenanopore while the other reservoir is connected to an outlet from thenanopore. In operation of the nanopore sensor for local electricalpotential measurement detection of species translocation through thenanopore, one or more objects of a species, such as molecules, areprovided in a fluidic solution in one of the reservoirs fortranslocation through the nanopore to the other of the two reservoirs.For many applications, and in particular for molecular sensingapplications, it can be preferred to provide the molecules or otherspecies objects in an ionic fluidic solution in one of the reservoirs.

The nanopore is provided as an aperture, gap, or other hole in thesupport structure and is provided with an extent, or for correspondingthe geometry, a diameter, that is suitable for sensing species objectsof interest. For example, for sensing molecular nanopore translocation,a nanopore of less than about 100 nm can be preferred, and a nanopore ofless than 10 nm, 5 nm, or 2 nm can be more preferred. As discussedbelow, a nanopore of even 1 nm can be suitable and even preferred forsome molecular sensing applications.

The reservoirs or other components of the nanopore sensor are configuredto provide a driving force for moving objects of a species, such asmolecules, through the nanopore from one of the reservoirs to the otherof the reservoirs. For example, electrodes 13, 15 can be provided in acircuit with voltage and current elements 16, 18 to produce anelectrophoretic force between the reservoirs for electrophoreticallydriving a fluidic solution, such as an electrically conductive ionicsolution, and the species in the solution, through the nanopore from onereservoir to the other reservoir. To enable electrophoretic driving ofthe species through the nanopore, the fluidic solutions of thereservoirs can be provided as electrically conductive ionic solutionshaving pH and other characteristics that are amenable to the species inthe solution. Thereby an electrical circuit can be connected with thereservoir solutions in series through the nanopore, with electrodes 13,15 as shown in the figures, providing an electrical voltage bias betweenthe solutions, across the nanopore.

As shown in FIG. 1A, there can be provided in the nanopore sensor atransduction element that senses the electrical potential local to thesite of the element and that develops a characteristic that isindicative of that local electrical potential. For example, anelectrical connection, such as device or region of a device and/orcircuit 7, a wire, or combination of circuit elements, that senses theelectrical potential local to the site of the device and/or circuit 7can be provided, to develop a signal indicative of local electricalpotential. The location of the electrical potential sensing can be in areservoir, on a surface of the support structure, or other locationwithin the nanopore sensor.

For example, as shown in FIG. 1B, there can be provided a circuit 20that includes, e.g., a transistor device 22, having a source, S, adrain, D, and a channel region 24. The channel region 24 is in thisexample physically disposed at a location in the nanopore sensorenvironment at which a local electrical potential measurement is to bemade. This physical location of the channel region 24 of the transistorcan be at any convenient and suitable site for accessing localelectrical potential.

In the example arrangements of FIGS. 1A-1B, an electrical potentialsensing circuit is configured local to the trans reservoir to provide atransistor or other device that measures the electrical potential localto the trans reservoir at the trans reservoir-side of the nanopore 12.Alternatively, as shown in FIG. 1C, an electrical potential sensingdevice or circuit 7 can be configured at the cis reservoir side of thenanopore. Here, e.g., as shown in FIG. 1D, there can be provided acircuit including a transistor 24 or other device for measuringelectrical potential local to the cis reservoir at the cis reservoirside of the nanopore 12.

In a further example alternative configuration, as shown in FIG. 1E,there can be included two or more circuits 20 a, 20 b, etc., with, e.g.,transistors 22 a, 22 b that sense the electrical potential at two ormore locations in the nanopore sensor system, such as each side of thenanopore membrane. Depending on the physical implementation of theelectrical potential sensing circuit, the electrical potential at thetwo sides of the nanopore membrane 14 can thereby be measured with thisarrangement. This is an example configuration in which is enabled ameasurement of the difference in local potential between two sites inthe nanopore sensor. It is therefore intended that the term “measuredlocal electrical potential” refer to the potential at a single site inthe nanopore sensor, refer to a difference or sum in local electricalpotential between two or more sites, and refer to a local potential attwo or more sites in the nanopore sensor configuration.

The local electrical potential measurement can be made by any suitabledevice and/or circuit or other transduction element, includingbiological or other non-solid state transduction elements, and is notlimited to the transistor implementation described above. For example,as shown in FIG. 1F, there can be provided on the membrane 14 or othersupport structure a single electron transistor (SET) circuit 27. Thesource, S, and drain, D, regions of the SET are disposed on the membraneor other support structure, providing tunneling barriers to the SET 27.In the resulting quantum dot system, the electrical conductance throughthe SET 27 depends on the energy level of the SET with respect to theFermi level of the source, S, and drain, D. With the nanopore 12 locatedin the vicinity of the SET, the electrical potential, and correspondingenergy level, of the SET changes as species objects translocate throughthe nanopore, changing the conductance of the SET circuit.

In a further example, as shown in FIG. 1G, there can be provided on themembrane 14 or other structure a quantum point contact (QPC) system 29for making a local electrical potential measurement. In this system, anelectrically conductive region 31 is provided that forms source, S, anddrain, D, regions that are connected via a very thin conducting channelregion at the site of the nanopore 12. The channel region issufficiently thin that the electronic carrier particle energy statesthat are perpendicular to the channel region are quantized. As speciesobjects translocate through the nanopore, the Fermi level inside thethin conduction channel region changes, resulting in a change in thenumber of quantized states below the Fermi level, and a correspondingchange in QPC conductance.

Accordingly, the nanopore sensor is not limited to solid state nanoporeconfigurations with solid state voltage sensing devices. Biologicalnanopores and potential sensing arrangements can also be employed, e.g.,with a protein nanopore or other suitable configuration. For example, asshown in FIG. 1H, there can be provided a lipid bilayer membrane 31 inwhich is disposed a protein nanopore 33. A voltage-sensitive dye, e.g.,a fluorescent direct dye 37, is provided in the lipid bilayer. With thisarrangement, when a species object such as a molecule or polymertranslocates through the protein nanopore, the voltage drop across thelipid bilayer changes, and the fluorescence of the dye is modulated bythe voltage change. Optical detection or sensing of the dye fluorescenceand changes to that fluorescence provide sensing of the potential at themembrane location. Optical microscope or other arrangement can beemployed for making this potential measurement as an optical outputsignal from the nanopore sensor.

This lipid bilayer nanopore sensor is an example of a biologicalnanopore sensor that is based on sensing of the local potential at thesite of the nanopore. The method of local potential measurement fornanopore translocation detection is not limited to a particular solidstate or biological configuration and can be applied to any suitablenanopore configuration.

Referring to FIG. 2A, these configurations for measuring the localelectrical potential at one or more sites in a nanopore sensor can beemployed in a method for sensing the translocation of species throughthe nanopore. To explain the principle of this sensing, it isinstructive to model the nanopore sensor as a circuit 35 includingelectrical components corresponding to physical elements of the sensor,as shown in FIG. 2A. The cis and trans reservoirs can each be modeledwith a characteristic fluidic access resistance, R_(Trans), 36, R_(Cis),38. This access resistance is the fluidic resistance from the bulk ofthe reservoir solution to the site of the nanopore. The nanopore can bemodeled with a characteristic nanopore solution resistance, R_(Pore),that is the fluidic resistance of solution through the length of thenanopore between the two sides of the membrane or other structure inwhich the nanopore is disposed. The nanopore can also be modeled with acharacteristic capacitance C_(Pore), that is a function of the membraneor other support structure in which the nanopore is disposed. The accessresistance of both chambers and the nanopore solution resistance 40 arevariable.

In a nanopore sensor starting condition in which no species aretranslocating through the nanopore, the nanopore can be characterized bythe solution resistance, R_(pore), given above, and both fluidicreservoirs can be characterized by the access resistances of the transreservoir and the cis reservoir, R_(Trans) and R_(Cis), respectively.Then when a species object, such as a biological molecule 45,translocates through the nanopore 12 as shown in FIG. 2A, the solutionresistance, R_(Pore), of the nanopore and the access resistances,R_(Trans) and R_(Cis), of each of the reservoirs, change because themolecule in the nanopore at least partially blocks the passagewaythrough the nanopore length, changing the effective diameter of thenanopore. With such a blockage, the fluidic solution resistance of thenanopore and the access resistance of both reservoirs increase above theresistance of the nanopore and access resistance of both reservoirs withno molecule present in the nanopore.

The partial blockage of the nanopore by a species object effects thenanopore solution resistance and the reservoir access resistancesdifferently, as explained in detail below. As a result, the partialblockage of the nanopore by a translocating species causes acorresponding redistribution of electrical voltage occurs between thenanopore and the cis and trans reservoirs solutions, and the electricalpotential at sites throughout the nanopore sensor accordingly adjusts.The local electrical potential at both the sites denoted as A and B inFIG. 2A thereby changes accordingly with this change in nanoporesolution resistance and redistribution of voltage between the reservoirsolutions and the nanopore. A measurement of electrical potential ateither of these sites, or at another site of the nanopore sensorconfiguration, or a measurement of a difference in local potentialbetween two or more sites, thereby provides an indication of thetranslocation of the molecule through the nanopore.

The local electrical potential at a selected nanopore sensor site andchanges in this potential can be sensed by, e.g., changes in theconductance of the conducting channel in a transistor device. Transistorchannel conductance therefore can be employed as a direct indication ofthe electrical potential local to the physical location of thetransistor channel. Thus, the nanopore sensor arrangements of FIGS.1A-1B correspond to a local electrical potential measurement at site Ain the circuit 35 of FIG. 2A. The nanopore sensor arrangements of FIG.1C-1D correspond to a local electrical potential measurement at site Bin the circuit 35 of FIG. 2A. The nanopore sensor arrangement of FIG. 1Ecorresponds to a local electrical potential measurement at both sites Aand B in the circuit 35 of FIG. 2A, and enables a determination of thedifference between the potential at those two sites.

An electrical circuit equivalent of the example configuration of FIG. 1Bis shown in FIG. 2B. Here is represented the access resistances of thecis and trans reservoirs, R_(Cis), R_(Trans), respectively, and thefluidic solution resistance, R_(Pore), of the nanopore. The location ofa device for measuring local potential, e.g., the channel of atransistor 22, is here positioned at the site A in FIG. 2A, providing alocal electrical potential indication in the trans reservoir at thetrans reservoir side of the nanopore. With this arrangement, as speciesobjects such as molecules translocate through the nanopore, the outputsignal of the electrical potential measurement circuit can be monitoredfor changes in electrical potential, corresponding to changes in thestate of the nanopore and the presence or absence of one or more objectsin the nanopore.

This analysis can be applied to any nanopore sensor in which there isprovided a local electrical potential measurement circuit and/or device.The analysis is not limited to the FET implementation described above,and is applicable to all of the implementations shown above, as well asothers. All that is required is the provision of a device or circuitthat makes a local electrical potential measurement as species objectstranslocate through the nanopore.

To further analyze the nanopore sensor system parameters, the nanoporesensor can be modeled as shown in the schematic representation of FIG.3A. Several assumptions can be employed to enable an analyticalcalculation. First, the geometrical change of the membrane, nanopore, orother region of the nanopore sensor that is caused by the inclusion of alocal potential sensing device or circuit can be ignored and thepotential sensing device can be modeled as a point potential detector.The reservoirs are assumed to include electrically conductive ionicsolutions. The two reservoir solutions are specified to be characterizedby differing ionic concentrations. With this specification, theconcentration distribution through the nanopore system is determined bythe steady state diffusion that is driven by the cis/trans reservoirconcentration difference. A further assumption can be made byapproximating the buffer concentration distribution and electricalpotential as being constant in small hemispheres on both sides of thenanopore. The nanopore sensor is assumed to be in steady state. Underthese conditions, the diffusion equations of the nanopore sensor aregiven as:

$\begin{matrix}\{ \begin{matrix}{\frac{\partial C}{\partial t} = 0} & \begin{pmatrix}{{For}\mspace{14mu} {both}\mspace{14mu} {chambers}\mspace{14mu} {and}\mspace{14mu} {inside}} \\{{the}\mspace{14mu} {nanopore}}\end{pmatrix} \\{{{r\frac{\partial^{2}{C(r)}}{\partial r^{2}}} + {2\frac{\partial{C(r)}}{\partial r}}} = 0} & ( {{For}\mspace{14mu} {both}\mspace{14mu} {chambers}} ) \\{\frac{\partial{C(z)}}{\partial z} = {const}} & ( {{Inside}\mspace{14mu} {the}\mspace{14mu} {nanopore}} )\end{matrix}  & (1)\end{matrix}$

Where C is concentration, t is time, r is location in a reservoir at apoint measured from the nanopore, and z is distance through the nanoporelength. If these diffusion equations are solved under the boundaryconditions that in the cis reservoir far away from the nanopore,C=C_(Cis), in the trans reservoir far away from the nanopore,C=C_(Trans), the flux is the same in the nanopore and for bothreservoirs, and the concentration is continuous at the nanopore openingin each reservoir, then the ionic concentration of the two reservoirsand the nanopore can be given as:

$\begin{matrix}\{ \begin{matrix}{{C_{C}(r)} = {C_{Cis} - {\frac{C_{Cis} - C_{Trans}}{4( {{2l} + d} )}\frac{d^{2}}{r}}}} & ( {{Cis}\mspace{14mu} {chamber}} ) \\{{C_{T}(r)} = {C_{Trans} - {\frac{C_{Trans} - C_{Cis}}{4( {{2l} + d} )}\frac{d^{2}}{r}}}} & ( {{Trans}\mspace{14mu} {chamber}} ) \\{{C_{P}(z)} = {C_{Trans} + {\frac{C_{Cis} - C_{Trans}}{2( {{2l} + d} )}( {{4z} + d} )}}} & ({Nanopore})\end{matrix}  & (2)\end{matrix}$

Here l and d are thickness of membrane or other support structure andnanopore diameter, respectively. Because the ionic concentrationdistribution is therefore known and the solution conductivity isproportional to the concentration, then the conductivity of solution, σ,is given as:

σ=Σ·C.   (3)

Here Σ is the molar conductivity of solution. Assuming the total currentis I, then the electrical potential drop through the nanopore sensor,with a cis reservoir voltage, V_(C), a trans reservoir voltage, V_(T),and a nanopore voltage, V_(P), can be given as:

$\begin{matrix}\{ \begin{matrix}{{{dV}_{C}(r)} = \frac{Idr}{2{\pi\Sigma}\; {C_{C}(r)}r^{2}}} & ( {{Cis}\mspace{14mu} {chamber}} ) \\{{{dV}_{T}(r)} = \frac{- {Idr}}{2{\pi\Sigma}\; {C_{T}(r)}r^{2}}} & ( {{Trans}\mspace{14mu} {chamber}} ) \\{{{dV}_{P}(r)} = \frac{4{Idz}}{{\pi\Sigma}\; {C_{P}(z)}d^{2}}} & ({Nanopore})\end{matrix}  & (4)\end{matrix}$

If these three equations are solved with boundary conditions that faraway from nanopore in the cis reservoir the electrical potential equalsthe voltage applied across the structure or membrane, i.e., atransmembrane voltage (TMV), to electrophoretically drive an objectthrough the nanopore, and that far away from nanopore in the transchamber, the potential is 0 V, then the voltages in the nanopore sensor,namely, the voltage in the cis reservoir, V_(C)(r), the voltage in thetrans reservoir, V_(T)(r), and the voltage in the nanopore, V_(P)(r),are given as:

$\begin{matrix}\{ \begin{matrix}{{V_{C}(r)} = {V + {\frac{2{I( {{2l} + d} )}}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln( {1 - \frac{( {C_{Cis} - C_{Trans}} )d^{2}}{4( {{2l} + d} )C_{Cis}r}} )}}}} \\{{V_{T}(r)} = {\frac{2{I( {{2l} + d} )}}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln( {1 + \frac{( {C_{Cis} - C_{Trans}} )d^{2}}{4( {{2l} + d} )C_{Trans}r}} )}}} \\{{V_{P}(r)} = {\frac{2{I( {{2l} + d} )}}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln( \frac{\begin{matrix}{{( {{4l} + d} )C_{Trans}} + {dC}_{Cis} +} \\{4( {C_{Cis} - C_{Trans}} )z}\end{matrix}}{2( {{2l} + d} )C_{Trans}} )}}}\end{matrix}  & (5)\end{matrix}$

Because the electrical potential is continuous at both nanopore openingsinto the reservoirs and because the total voltage applied is V,Expression (5) can be further simplified to:

$\begin{matrix}\{ \begin{matrix}{{V_{C}(r)} = {V + {\frac{V}{\ln ( {C_{Cis}/C_{Trans}} )}{\ln( {1 - \frac{d^{2}( {1 - {C_{Trans}/C_{Cis}}} )}{4( {{2l} + d} )r}} )}}}} \\{{V_{T}(r)} = {\frac{V}{\ln ( {C_{Cis}/C_{Trans}} )}{\ln( {1 + \frac{d^{2}( {{C_{Cis}/C_{Trans}} - 1} )}{4( {{2l} + d} )r}} )}}} \\{{V_{P}(r)} = {\frac{V}{\ln ( {C_{Cis}/C_{Trans}} )}{\ln( \frac{\begin{matrix}{{4l} + d + {{dC}_{Cis}/C_{Trans}} +} \\{4( {{C_{Cis}/C_{Trans}} - 1} )z}\end{matrix}}{2( {{2l} + d} )} )}}}\end{matrix}  & (6)\end{matrix}$

With this expression, the electric field, E_(P)(r) inside nanopore canbe given as:

$\begin{matrix}{{E_{P}(r)} = {\frac{{dV}_{P}(r)}{dz} = {\frac{4{V( {{C_{Cis}/C_{Trans}} - 1} )}}{\ln ( {C_{Cis}/C_{Trans}} )}{\frac{1}{{4l} + d + {{dC}_{Cis}/C_{Trans}} + {4( {{C_{Cis}/C_{Trans}} - 1} )z}}.}}}} & (7)\end{matrix}$

With this expression, the electrical potential change at the transreservoir side of the nanopore can be estimated by the electricalpotential change due to a reduction in the nanopore area, A, by thepresence of a species object, such as a molecule, in the nanopore, as:

$\begin{matrix}{{{{{{{{\delta \; V_{T}}}_{d/2} = \frac{\partial V_{T}}{\partial A}}}_{d/2}\delta \; A} = {\frac{2\delta \; {AV}}{{\pi ln}( {C_{Cis}/C_{Trans}} )}\frac{( {{4l} + d} )( {{C_{Cis}/C_{Trans}} - 1} )}{( {{2l} + d} )( {{d^{2}( {{C_{Cis}/C_{Trans}} - 1} )} + {4( {{2l} + d} )r}} )}}}}_{d/2} = {\frac{2\delta \; {AV}}{{\pi ln}( {C_{Cis}/C_{Trans}} )}\frac{( {{4l} + d} )( {{C_{Cis}/C_{Trans}} - 1} )}{( {{2l} + d} )( {{d^{2}( {{C_{Cis}/C_{Trans}} + 1} )} + {4{ld}}} )}}} & (8)\end{matrix}$

Here δA is the cross-sectional area of the molecule.

The resistances of the nanopore sensor, namely, R_(Cis), R_(Trans), andR_(Pore), can be computed based on the above expressions for voltagedrop across the reservoirs and the nanopore as:

$\begin{matrix}\{ \begin{matrix}{R_{Cis} = {\frac{{- 2}( {{2l} + d} )}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln ( {1 - \frac{( {C_{Cis} - C_{Trans}} )d}{2( {{2l} + d} )C_{Cis}}} )}}} \\{R_{Trans} = {\frac{2( {{2l} + d} )}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln ( {1 + \frac{( {C_{Cis} - C_{Trans}} )d}{2( {{2l} + d} )C_{Trans}}} )}}} \\{R_{Pore} = {\frac{2( {{2l} + d} )}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln ( \frac{{( {{4l} + d} )C_{Cis}} + {dC}_{Trans}}{{( {{4l} + d} )C_{Trans}} + {dC}_{Cis}} )}}}\end{matrix}  & (9)\end{matrix}$

So, the total resistance and ionic current of the nanopore sensor aregiven as:

$\begin{matrix}\{ {\begin{matrix}{R = {{R_{Cis} + R_{Trans} + R_{Pore}} = {\frac{2( {{2l} + d} )}{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}}{\ln ( \frac{C_{Cis}}{C_{Trans}} )}}}} \\{I = {{V/R} = \frac{{{\pi\Sigma}( {C_{Cis} - C_{Trans}} )}d^{2}V}{2( {{2l} + d} ){\ln ( {C_{Cis}/C_{Trans}} )}}}}\end{matrix}.}  & (10)\end{matrix}$

With these expressions, it is demonstrated that the electricalcharacteristics of the nanopore sensor, and in particular thedistribution of electrical potential in the sensor, depends directly onthe ionic concentration of the fluidic solutions in the cis and transreservoirs. Specifically, the ratio of the reservoir solutionconcentrations directly impacts the magnitude of the change in localpotential due to species translocation through the nanopore.

FIGS. 3B-3E are plots of electrical potential and electric field in thenanopore, demonstrating these conditions. Given a cis/trans buffersolution concentration ratio=1:1, a 50 nm-thick nitride membrane, a 10nm diameter nanopore in the membrane, and a 1 V transmembrane voltage,i.e., 1 V applied between the solutions in the two reservoirs, then theelectrical potential in the nanopore as a function of distance from thenanopore opening at the cis reservoir is plotted in FIG. 3B, based onExpression (6) above. That same potential is plotted in FIG. 3C for acondition in which the cis/trans buffer solution concentration ratio isinstead 100:1. Note the increase in electrical potential at a givennanopore location for the unbalanced buffer solution ratio at pointscloser to the lower-concentration reservoir.

FIG. 3D is a plot of the electric field in the nanopore under theconditions given above, here for a balanced buffer solution ratio, basedon Expression (7) above. That same electric field profile is plotted inFIG. 3E for a condition in which the cis/trans buffer solutionconcentration ratio is instead 100:1. Note the increase in electricalpotential at a given nanopore location for the unbalanced buffersolution ratio, and that the electric field is dramatically stronger atpoints closer to the low concentration, higher resistance, reservoir.

With this finding, it is discovered that with a condition in which thereservoir solutions are both provided as electrically-conductive ionicsolutions of the same ionic concentration, the ratio of the accessresistance of the cis reservoir, R_(Cis), the access resistance of thetrans reservoir, R_(Trans), and the solution resistance of the nanopore,R_(Pore), are all fixed and the nanopore resistance is much larger thanthe reservoir access resistances. But under non-balanced ionconcentration conditions, the reservoir having a lower ionicconcentration has a larger access resistance, that can be on the orderof the nanopore resistance, while the higher-ionic concentrationreservoir resistance becomes comparably negligible.

Based on a recognition of this correspondence, it is herein discoveredthat to maximize a local potential measurement in the nanopore sensor,it is preferred that the ionic reservoir solutions be provided withdiffering ion concentrations. With this configuration of unbalancedionic concentration, the local potential measurement is preferably madeat a site in the reservoir which includes the lower ionic concentration.It is further preferred that the buffer concentration of the lower-ionconcentration solution be selected to render the access resistance ofthat reservoir of the same order of magnitude as the nanopore resistanceand much larger than the resistance of the high-ion concentrationsolution, e.g., at least an order of magnitude greater than that of thehigh-ion concentration solution, so that, for example, if the localpotential measurement is being made in the trans reservoir:

R _(T) , R _(P) >>R _(C)   (11)

Based on this discovery then, for a given nanopore diameter, which setsthe nanopore resistance, R_(P), it is preferred to decrease the ionicsolution buffer concentration of the reservoir designated for localpotential measurement to a level at which the access resistance of thatreservoir is of the same order of magnitude as the nanopore resistance.This reservoir access resistance should not dominate the nanopore sensorresistance, but should be on the order of the nanopore resistance.

This condition can be quantitatively determined directly by electricallymodeling the nanopore sensor components in the manner described above.Based on Expression (8) above, there can be determined the ratio ofsolution concentrations that maximize the potential change duringnanopore translocation of a selected object for given nanopore sensorparameters. For example, FIG. 4A is a plot of Expression (8) for a 50nm-thick nanopore membrane and a configuration of a 1 V TMV forelectrophoretic species translocation as a dsDNA molecule translocatesthrough the nanopore. The potential change is shown as a function of theC_(Cis)/C_(Trans) ionic concentration ratio for various nanoporediameters below 10 nm. From this plot, it is found that the localpotential change in the trans reservoir is maximized for a ˜100:1C_(Cis)/C_(Trans) chamber buffer concentration ratio for any nanoporediameter modeled here. FIG. 4B is a plot of the corresponding calculatedpotential change distribution in the trans reservoir for a 10nm-diameter nanopore at 1 V TMV for the selected 100:1 C_(Cis)/C_(Trans)solution concentration ratio.

This demonstrates that based on the discovery herein, for a givenreservoir site that is selected for making electrical potentialmeasurements, the ratio of ionic fluid buffer concentration in the tworeservoirs is to be selected with the lower buffer concentrationsolution in the measurement reservoir, to maximize the amplitude of theelectrical potential changes at that selected measurement site. Thedistribution of this resulting potential change is highly localizedwithin several tens of nanometers of the nanopore, as shown in FIG. 4B.For the example 100:1 C_(Cis)/C_(Trans) solution concentration ratio andnanopore parameters given just above, it can be determined, e.g., basedon Expression (9) above, that the access solution resistance of thetrans reservoir and the solution resistance of the nanopore are indeedwithin the same order of magnitude.

With this arrangement of reservoir fluidic solution bufferconcentrations and potential measurement configuration, it is noted thatthe local potential sensing technique of produces a local potentialmeasurement signal that depends on the trans-membrane voltage (TMV) andthe ionic current signal. Other sensor based nanopore technologiesgenerally rely on a direct interaction between a translocating speciesand the nanopore sensor through, e.g., electrical coupling or quantummechanical tunnelling. For these techniques, the nanopore output signalis typically not directly related to the TMV or ionic current and shouldnot change significantly when the TMV is changed. In contrast, in thelocal potential measurement system herein, the nanopore sensor signal isproportional to the TMV and can be regarded as a linear amplification ofthe ionic current signal. As a result, both the local potentialmeasurement signal and the ionic current signal amplitudes depend on theTMV linearly, but the ratio between them is a constant for a givennanopore geometry and reservoir solution concentrations, as evidenced bythe expressions given above.

An advantage of the local potential measurement method is thecharacteristically high-bandwidth capability of the measurement with lownoise. Low signal bandwidth is one of the issues that limits directnanopore sensing by the conventional ionic current blockage measurementtechnique, due to the difficulties of high bandwidth amplification ofvery small measured electrical current signals. This can be particularlytrue for a small nanopore when employed for DNA sensing. In the localpotential sensing method, a large local electrical potential signal ismeasured instead of a small current signal, so the signal bandwidth isnot limited by the capabilities of a current amplifier. As a result,high-bandwidth signal processing electronics can be integrated on asolid state nanopore sensing structure.

Further, except for intrinsic shot noise and Johnson noise, the majorityof noise contributions to an ionic current blockage measurementtechnique are introduced through the capacitive coupling cross ananopore membrane and this capacitive coupling component of noise can beoverwhelming at certain stages of nanopore operation. Conventionally, avery small membrane area exposure to a reservoir solution is required inan effort to minimize noise. In the local potential measurement methodherein, because the local potential signal decays within a few tens ofnanometers around the nanopore for reasonable reservoir concentrationratios, the local potential measurement signal is only affected bycapacitive coupling between reservoir solutions within this localvolume. Therefore, the majority of capacitive coupling noise isautomatically rejected in the local electrical potential measurementsensing method.

Referring to FIGS. 4C-4D, the reservoir buffer solution concentrationratio can be selected to optimize the signal bandwidth of the nanoporesensor. Given that the local potential measurement is to be made in thetrans side of the nanopore, then the cis reservoir solutionconcentration is set as high as reasonable, e.g., about 4 M, about asaturated solution, to minimize the nanopore solution resistance. Then,the signal noise as a function of bandwidth is analyzed, e.g., based onthe plot of FIG. 4C. Here are plotted the various contributions to noiseas well as the signal expected for a fluidic nanopore operation. Theplot labelled “free space” refers to a computation based on free-spacemolecular size. The plot labelled “Bayley” refers to computation basedon molecular size from previous work by Bayley et al, in J. Clarke etal., “Continuous Base Identification for Single-Molecule Nanopore DNASequencing,” Nature Nanotechnology, N. 4, pp. 265-270, 2009. The twosignal lines are the minimum signal difference that is attained betweenthe four DNA bases, which minimum signal exists between the A and the Tbases. Here the nanopore is given as a 1 nm-diameter nanopore in agraphene membrane, with a 4 M cis reservoir solution concentration, abuffer concentration ratio between the reservoirs of 50:1, and a voltagenoise density of about 10⁻⁹ V/√Hz. The dielectric loss factor forgraphene is unknown, so 1 was used for convenience. Finding the crosspoint of the signal and total noise in the plot sets the 1:1signal-to-noise ratio (S/N). This is the highest possible signalbandwidth. For example, for the fluidic nanopore operation, the 1:1 S/Nratio is at a bandwidth of about 100 MHz. A bandwidth greater than about50 MHz can be preferred as well as the 100 MHz bandwidth.

Referring to the plot of FIG. 4D, the 100 MHz bandwidth corresponds toreservoir solution concentration ratio of about 50:1, where the localpotential measurement is to be made in the low-concentration reservoirside of the nanopore. For the nanopore sensor parameters used in thisexample, any reservoir concentration ratio higher than about 50:1 willdecrease the bandwidth. Any concentration ratio lower than about 50:1will decrease the signal-to-noise ratio. Therefore, it is discoveredherein that the bandwidth can be optimized and there exists anoptimization point of reservoir concentration ratio. The reservoirsolution concentration ratio is therefore selected based on a trade-offbetween the characteristic noise of the nanopore sensor and the desiredoperational bandwidth of the nanopore sensor. It is to be recognizedtherefore that to minimize noise, the reservoir solution concentrationratio can be increased, but that the bandwidth may be correspondinglyreduced. Alternatively, electronic signal processing, such as low-passfiltering, or other processing of the signal, can be employed.

It is further to be recognized that in general, a smaller nanoporeproduces a larger signal for a given species object to translocatethrough the nanopore. For applications such as sensing a particularmolecule, such as DNA, however, the nanopore extent is preferably sizedbased on the molecule, and the tuning of the reservoir concentrationratio is made accordingly.

The reservoir buffer solution concentration ratio can also be selectedto produce a signal decay length, measured from the site of thenanopore, that accommodates a selected local potential measurementdevice. It is recognized that the decay length of the signal should besufficiently large to accommodate the arrangement of a potentialmeasurement device within the decay length. FIG. 4E is a plot of signaldecay length for a range of buffer concentration ratios, given that thelocal potential measurement is to be made on the trans reservoir side ofthe nanopore. The plot is based on the circuit model shown inset in theplot.

Based on this analysis, it is shown that at concentration ratios greaterthan about 20 or 30, there is produced a sufficient decay length toaccommodate a device that can measure the local electrical potentialwithin the decay length. At concentration ratios greater than about50:1, ample decay length is provided for making a potential measurementwithin the decay length. A signal decay length greater than about 5 nmcan be preferred, as well as a signal decay length of, e.g., about 10 nmand about 20 nm.

Turning to implementation of a local potential measurement device, asexplained above, a local electrical potential measurement can be made inthe nanopore sensor with any suitable device or circuit thataccommodates the nanopore implementation. For many applications, ananowire-based FET device can be a well-suited device, but such is notrequired herein. The SET, QPC, lipid bilayer, or other device andnanopore implementation, whether biological or solid state, can beemployed. Any circuit or device that enables a local potentialmeasurement can be employed.

In one example, a nanowire FET can be configured at the site of thenanopore as shown in FIG. 5. In this nanowire implementation 60, thereis provided a nanowire 62 on the support structure or membrane 14 inwhich is disposed the nanopore 12. The nanowire can be formed of anysuitable electrically conducting or semiconducting material, includingfullerene structures and semiconducting wires. The term “nanowire” asused herein refers to an electrical conduction channel that ischaracterized by a width that is compatible with the signal decay lengthmeasured from the nanopore site as described above. The channel width ispreferably on the same order of magnitude as the decay length and can belarger. The nanowire can be made from any semiconductor material that isstable in the selected reservoir solution.

FIG. 6 is a perspective view of an example implementation 65 of thenanopore sensor of FIG. 5. Here is shown the nanowire 62 provided on amembrane 14 that is self-supported and that is disposed on a supportstructure 64 such as a substrate. The nanowire is provided on themembrane with a nanopore extending through the thickness of the nanowireand the membrane. As shown in FIGS. 5 and 6, the nanopore 12 does notextend across the width of the nanowire. There is a region 66 of thenanowire that is unbroken along the extent of the nanopore so thatelectrical conduction is continuous along the length of the nanowire. Ametallization region or other electrically conducting region is providedat each end of the nanowire to form source (S) and drain (D) regions.With this configuration, the nanopore sensor can be configured with cisand trans reservoirs as shown for detecting translocation of speciesfrom one reservoir through the nanopore to the other reservoir.

Referring also to FIGS. 7A-7B, the membrane and nanowire configurationcan be implemented in a variety of alternative arrangements, and themembrane is not required for applications in which a nanowire materialis self-supporting and can itself function as a support structure inwhich the nanopore is disposed. For example, as shown in FIGS. 7A-B, ina graphene-based nanopore sensor 68, there can be provided a membrane70, which in turn supports a graphene membrane 72. The graphene membrane72 is self-supported across an aperture in the membrane 70. The graphenemembrane in turn supports a nanowire 62, with a nanopore 12 extendingthrough the thickness of the nanowire and the graphene, and the nanowireremaining continuous along some point of the nanowire. As shown in FIGS.8A-8B, this arrangement can be altered, with the nanowire 62 insteaddisposed under the graphene layer 72, on a membrane 70.

In an alternative graphene-based nanopore sensor 75, as shown in FIGS.9A-9B, there can be configured a support structure, such as a membrane70, on which is disposed a graphene layer 72 that functions to provide astructure in which a nanopore 12 is configured and that itself functionsto provide a nanowire. The graphene can be provided in any suitablegeometry that provides the requisite nanowire at the site of thenanopore 12. In this configuration, the graphene layer 72, due to itsthickness and conductivity, senses the local electrical potential onboth sides of the nanopore, i.e., the conductance of the graphene layerchanges as a function of the local potential in both the trans and cisreservoirs. The nanopore sensor signal of a local potential measurementis therefore for this graphene-based nanopore sensor an indication ofthe difference between the cis and trans reservoir potentials.

As demonstrated by these example arrangements, the membrane, nanowire,and support structure can be configured with any in a wide range ofmaterials combinations and thicknesses. For many applications, it can bepreferred that the structure in which the nanopore is disposed be asthin as possible, and preferably no thicker than the extent of a speciesobject, or object region to be detected. Example membrane materialsinclude nitrides, oxides, graphene, plastics, or other suitablematerial, which can be electrically insulating or electricallyconducting.

As shown in FIGS. 10A-10D, for a nanowire implementation, the nanoporeis provided at the location of a nanowire 62 such that an unbroken,continuous path for electrical conduction is provided through thenanowire. The nanopore can be provided at a central region of thenanowire, as depicted in FIG. 10A, can be provided at an edge of thenanowire, as depicted in FIGS. 10B-10C, or can be provided at a sitenear to or adjacent to the nanowire, as depicted in FIG. 10D. In allcases, a continuous path for electrical conduction is provided throughthe nanowire.

In the nanopore arrangements of FIGS. 10A-10C, it is found that thesensitivity of the nanopore region is also significantly enhancedcompared to the sensitivity of the same region prior to nanoporedrilling. This sensitivity localization can be understood by a modelaccounting for the reduction of the cross-sectional area of the nanowireas a conduction channel, assuming all other material properties, such asdoping level and mobility remain unchanged. The reduced cross-sectionalarea of the nanowire increases the resistance of the nanopore region andtherefore alleviates series resistance and signal attenuation from otherportions of the nanowire. Quantitatively, this sensitivity enhancementat the nanopore region can be obtained from the following equation for arectangular-shaped nanopore as an example:

$\begin{matrix}{\Delta = {( \frac{\rho_{0}L}{{\rho ( {L - L_{0}} )} + {\rho_{0}L_{0}}} )^{2}.}} & (12)\end{matrix}$

Here, Δis the sensitivity enhancement defined as the sensitivity of thedevice with a nanopore divided by the sensitivity without the nanopore,and ρ₀ and ρ are the linear resistivities of the nanowire conductionchannel with and without the nanopore, respectively. L is the totalchannel length and L₀ is the channel length of the nanopore region,which for this square example is equal to the side length of thenanopore along the nanowire axial direction. For other portions ofnanowire, because all parameters remain the same but the total channelresistance is increased slightly due to the nanopore, the sensitivityshould decrease slightly after nanopore drilling. The combination ofincreased sensitivity at the nanopore region and decreased sensitivityof all other nanowire portions makes the sensitivity of a nanoporesensor enhanced, self-aligned and localized at the nanopore.

In fabrication of the nanopore sensor, first considering ananowire-based solid state nanopore sensor, a short-channel nanowire canbe preferred, and for many applications, a silicon nanowire (SiNW) canbe preferred because the SiNW has been demonstrated as an excellentelectrical potential and charge sensor for sub-cellular and single-viruslevel signaling with remarkable stability in solution. To minimizesignal attenuation from channel series resistance, the SiNW channel canbe reduced, if desired, to less than about 200 nm by nickel solid-statediffusion. SiNWs can be fabricated by, e.g., chemical vapor deposition,or other suitable process, and disposed on a selected membrane, such asa nitride membrane, by solution. For many applications, acommercially-available nitride membrane chip can be suitably employed.Electron beam lithography or optical lithography can be employed forproducing source and drain electrodes at ends of the nanowire. Allelectrodes and electrical contacts are to be passivated with, e.g., anitride or oxide material, and such can be accomplished after metalevaporation and before lift-off processes. The nanopore can be producedat a selected site by, e.g., electron beam, or by other beam species oretching process that produces a selected nanopore dimension.

In fabrication of a graphene-based nanopore sensor including a nanowirestructure on top of the graphene membrane, like the graphene-basednanopore sensor of FIGS. 7A-7B, first a membrane, such as a nitridemembrane, is processed to form a micron-sized aperture in the membrane,e.g., by electron beam lithography or photolithography and reactive ionetching (RIE). Then a graphene sheet or piece is disposed on the nitridemembrane, covering the aperture, to form a graphene membrane. Thegraphene sheet can be synthesized by CVD or other process, or producedby mechanical exfoliation, and transferred to the nitride membrane, overthe nitride membrane aperture.

Electron beam lithography or photolithography can then be conducted withmetal evaporation to define electrodes in the conventional manner on thenitride membrane. Dielectrophoresis or other suitable process can thenbe employed to align a nanowire, such as a silicon nanowire, on top ofthe graphene membrane at the location of the aperture in the nitridemembrane. Electron beam lithography or photolithography can then beconducted with metal evaporation to define the source and drain contactsat ends of the SiNW. Thereafter, excessive graphene can be removed byelectron beam lithography or photolithography and, e.g., UV-ozonestripper, oxygen plasma, or other suitable method to remove graphenefrom regions outside the intended graphene membrane location. Finally, ananopore is produced through a site at the nanowire and the underlyinggraphene membrane by, e.g., an electron beam.

In fabrication of a graphene-based nanopore sensor including a graphenemembrane that is on top of a nanowire FET structure, like thegraphene-based nanopore sensor of FIGS. 8A-8B, a suitable structure canbe employed for configuring the arrangement, e.g., with asilicon-on-insulator chip (SOI). In this example, an aperture is firstformed through the backside thick silicon portion of the SOI chip, e.g.,by XF₂ etching, stopping on the oxide layer, to form an oxide-siliconmembrane. Then electron beam lithography or photolithography is employedto remove the oxide layer from the SOI chip in a smaller apertureregion, producing a membrane of silicon from the thin silicon region ofthe SOI chip. This silicon membrane is then etched to form a nanowire ofsilicon, e.g., with electron beam lithography or photolithography andchemical etching or RIE. In one example, a dove-tail-shaped Si piece isformed as shown in FIG. 8B, aligned with the aperture in the oxidemembrane of the SOI chip.

Electron beam lithography or photolithography can then be conducted withmetal evaporation to define electrodes in the conventional manner on theoxide layer. Then a graphene sheet or piece is disposed on the oxidemembrane, covering the aperture, to form a graphene membrane over thesilicon nanowire. The graphene sheet can be synthesized by CVD or otherprocess, or produced by mechanical exfoliation, and transferred to theoxide membrane, over the SiNW and oxide membrane aperture. It isrecognized that because the graphene sheet is being overlaid on top ofthe patterned silicon layer, the graphene piece may not be flat. Ifleakage is a concern for this configuration, then a thin layer of, e.g.,SiO_(x) can be coated around the graphene edges to form a sealed edgecondition.

Thereafter, excessive graphene can be removed by electron beamlithography or photolithography and, e.g., UV-ozone stripper, oxygenplasma, or other suitable method to remove graphene from regions outsidethe intended graphene membrane location. Finally, a nanopore is producedthrough a site at the overlying graphene and the silicon nanowire, e.g.,by electron beam, in relation to the location of the most narrow Sigeometry.

In fabrication of a graphene-based nanopore sensor like that depicted inFIG. 9A, first a membrane, such as a nitride membrane, is processed toform a micron-sized aperture in the membrane, e.g., by electron beamlithography or photolithography and reactive ion etching (RIE). Then agraphene sheet or piece is disposed on the nitride membrane, coveringthe aperture, to form a graphene membrane. The graphene sheet can besynthesized by CVD or other process, or produced by mechanicalexfoliation, and transferred to the nitride membrane, over the nitridemembrane aperture.

Electron beam lithography or photolithography can then be conducted withmetal evaporation to define source and drain electrodes in theconventional manner on the graphene membrane. Thereafter, the grapheneis patterned in a dovetail or other selected shape by electron beamlithography or photolithography and, e.g., UV-ozone stripper, oxygenplasma, or other suitable method to produce a narrow graphene region inthe vicinity of the selected site for a nanopore. Finally, a nanopore isproduced through the graphene membrane by, e.g., electron beam.

In fabrication of a SET-based nanopore sensor like that of FIG. 1F, anysuitable membrane material, both electrically conductive andelectrically insulating, can be employed. A nitride membrane structureor other structure can be employed, such as a graphene membrane orcombination graphene-nitride membrane structure as-described above. Ifan electrically conducting membrane material is employed, it can bepreferred to coat the material with an insulating layer, such as anoxide or nitride layer, on the side of the membrane on which the SET isto be formed. Electron beam lithography and metal evaporation techniquescan then be employed to form the source and drain regions and the SETregion out of a suitable metal. A nanopore can then be formed at thelocation of the SET in the manner given above. If an insulating layer isprovided on an electrically conducting membrane material and theinsulating layer coated the length of the nanopore through the membrane,then it can be preferred to remove that insulating material from thenanopore sidewall by, e.g., HF or other suitable etching, from thebackside of the nanopore, to remove the insulator layer from thenanopore and from the adjacent vicinity of the nanopore.

In fabrication of a QPC arrangement like that of FIG. 1G with ananopore, an SOI structure can be employed, removing the thick siliconlayer in the manner described above, and then using electron beamlithography to define the top silicon layer structure in the QPCarrangement. The nanopore can then be formed through the membrane in themanner given above.

These example processes are not intended to be limiting and are providedas general examples of techniques for producing nanopore sensors. Anysuitable membrane material and device material can be employed. For manyapplications it can be preferred that a nonconducting membrane materialbe employed in conjunction with a conducting nanowire material. Thelocal electrical potential measurement method can be applied to anynanopore sensor and is not limited to a particular configuration ormethod for producing such configuration.

In each of these example processes, it is preferred that the dimensionsof the nanopore be selected based on a selected ratio of the reservoirbuffer solution concentrations, to achieve a desired electricalpotential measurement in the manner described above, in conjunction withconsideration for the species objects to be investigated with thenanopore sensor. The analytical expressions above can be employed todetermine an optimum nanopore size for a given species to be detected bytranslocation through the nanopore, in concert with the other nanoporesensor parameters and operation, for enabling electrical potentialmeasurement for nanopore sensing of the species.

This is particular important for maximizing the ability to distinguishbetween different species objects as nanopore translocation of theobjects is conducted. For example, the graphene-based nanopore sensorsdescribed above are particularly attractive for sensing molecularspecies such as DNA and other biopolymer species because the graphenethickness is on the order of a DNA base extent. But because graphene iselectrically gated on both sides of the graphene by the cis and transreservoir solutions, and the electrical potential in the two reservoirsis opposite, the sum of electrical potentials that is indicated by thegraphene potential measurement is smaller than that indicated by theimplementation of a nanowire on one side of a membrane. But for a smallnanopore, e.g., of about 1 nm in diameter, and with a sufficiently largeratio in buffer concentration between the cis and trans reservoirs, thesum of electrical potentials that is indicated by the graphene potentialmeasurement is comparable to that of a nanowire nanopore sensor.

Based on Expression (8) above, it can be shown that a graphene nanoporesensor enables local potential measurements that distinguish between theA, G, C, and T DNA bases. The following table presents thecross-sectional areas of each of these DNA bases, including the DNAbackbone, based on previous work as given, e.g., by M. Zwola et al.“Colloquium: Physical Approaches to DNA Sequencing and Detection,”Review of Modern Physics, No. 80, pp. 141-165, 2008.

TABLE I Base + backbone Cross-sect. Area (nm²) A 0.4731 G 0.5786 T0.5140 C 0.3932

Given a graphene effective thickness in solution of about 0.6 nm and aconcentration ratio of about 50:1 between the cis and trans reservoirbuffer solution ionic concentrations, then the local potential measuredby the nanopore sensor is as shown in the plots of FIG. 11 as a functionof nanopore diameter. As shown in the plot, this demonstrates that thegraphene-based nanopore sensor configured with differing cis and transreservoir solution concentrations provides a local potential measurementsignal difference of millivolts between each of the different bases,e.g., at least about 5 mV, and enables the ability to identify bases asthe bases translocate through the graphene nanopore.

EXAMPLE I Fabrication of a SiNW FET Device For Nanopore Sensing

SiNWs were synthesized using an Au-nanoparticle-catalyzed chemical vapordeposition (CVD) method. 30 nm-diameter gold nanoparticles (Ted PellaInc.) were dispersed on a silicon wafer coated with a 600 nm-thick layerof silicon oxide (NOVA Electronic Materials Inc.). Boron-doped p-typeSiNWs were synthesized at 435° C. and 30 Torr, with 2.4 standard cubiccentimeters per minute (sccm) silane as a silicon source, 3 sccmdiborane (100 ppm in helium) as a boron dopant source and 10 sccm argonas the carrier gas. The nominal doping ratio was 4000:1 (Si:B) and thegrowth time was 20 minutes. The resulting SiNWs were dissolved inethanol by gentle sonication for ˜10 seconds. Then the NW solution wasdeposited onto a 50 nm-thick, 100 μm×100 μm silicon nitride TEM membranegrid (SPI supplies). Electron beam lithography and evaporation of a 60nm-thick layer of nickel were carried out to fabricate ˜1 μmspaced-apart source and drain electrodes on the nanowire. A layer ofthickness of about 75-100 nm of silicon nitride was then deposited byplasma enhanced CVD (NEXX Systems) on the chip immediately after metalevaporation, to passivate all electrodes.

Lift-off of the mask was then carried out to produce a nanowire on anitride membrane having passivated source and drain electrodes. Thestructure was then annealed by a rapid thermal processor (HeatPulse 610,Total Fab Solutions) in forming gas at 380° C. for 135 seconds to shrinkthe nanowire channel to an extent less than about 200 nm. Afterconductivity testing of the resulting SiNW FET, the structure wascleaned by UV-ozone stripper (Samco International Inc.) at 150° C. for25 minutes on each side. The structure was then loaded into a fieldemission transmission electron microscope (TEM) (JEOL 2010, 200 kV) anda nanopore of about 9 nm or 10 nm in extent was drilled by through thenanowire at a selected location by convergent high energy electron beaminto one spot for approximately 2-5 minutes. The nanopore was sited atthe edge of the nanowire, as depicted in the arrangement of FIG. 10B,whereby a substantial portion of the nanowire width was continuous.

EXAMPLE II Sensitivity Profiling of a SiNW FET Device For NanoporeSensing

The sensitivity of the SiNW FET sensor of the nanopore sensor wascharacterized by scanning gate microscopy (SGM). A SiNW FET device wasfabricated in accordance with the method of Example I, here with ˜2 μmlong channel length to accommodate the limited spatial resolution ofSGM. SGM was performed in a Nanoscope Ma Multi-Mode AFM (DigitalInstruments Inc.) by recording the conductance of the nanowire as afunction of the position of a −10 V biased conductive AFM tip(PPP-NCHPt, Nanosensors Inc.). The AFM tip was 20 nm above the surfaceduring SGM recording.

Prior to formation of a nanopore at the nanowire site, an SGM profilewas produced across the nanowire. Then a nanopore was formed at the edgeof the nanowire in the arrangement depicted in FIG. 10B. With thenanopore present, the SGM profile of the nanowire was again produced.The SGM profile was determined by averaging the conductance over theapparent width (˜100 nm) of the Si NW in a perpendicular direction usingWSxM software. FIG. 12 is a plot of sensitivity, defined as conductancechange divided by AFM tip gate voltage, along the nanowire beforenanopore formation and after nanopore formation. It is clear that thesensitivity of the device is sharply localized and aligned with thenanopore. More importantly, the sensitivity of the nanopore region isalso significantly enhanced compared to the sensitivity of the sameregion prior to nanopore formation.

EXAMPLE III Cleaning and Assembly of a Nanowire-nanopore Device ForNanopore Sensing

The nanowire-nanopore assembly produced by the method of Example I abovewas cleaned by UV-ozone stripper (Samco International Inc.) at 150° C.for 25 minutes on each side after formation of the nanopore. Thiscleaning process is preferred to remove any possible carbon depositionon the structure. Then the structure was annealed in forming gas at 250°C.-350° C. for 30 seconds to recover the conductance of the nanowire. Afurther 25-minute room temperature UV-ozone cleaning was performed oneach side of the structure to ensure hydrophilicity of the nanopore justbefore assembly.

To assemble the nanowire-nanopore structure with fluidic reservoirs forspecies translocation through the nanopore, PDMS chambers were sonicatedfirst in DI water, then 70% ethanol and finally pure ethanol, each for˜30 minutes and then stored in pure ethanol. Just before assembly, PDMSchambers were baked in a clean glass petri dish at ˜80° C. for ˜2 hoursto remove most of the absorbed ethanol.

A printed circuit board (PCB) chip carrier was produced for makingelectrical connection to the nanopore sensor, and was cleaned byScotch-Brite (3M) to remove the copper surface oxide and anycontaminants such as glue. The PCB was then sonicated in isopropylalcohol and then in 70% ethanol, each for ˜30 minutes. Gold solutionelectrodes were cleaned in piranha solution for ˜1 hour just beforeassembly.

The cleaned nanowire-nanopore structure was glued into a ˜250 μm-deepcenter pit of the PCB chip carrier using Kwik-Cast (World PrecisionInstruments, Inc.) silicone glue, with the device side surfaceapproximately flush to the surface of the rest of PCB chip carrier. Thesource and drain electrical contacts of the device were wired to copperfingers on the chip carrier by wire bonding (West-Bond Inc.). The frontPDMS chamber was formed of a piece of PDMS with a ˜1.8 mm hole in thecenter, with a protrusion of ˜0.5 mm around one side of the holeopening, for pressing against the nanopore membrane surface to ensure atight seal. The PDMS chambers were mechanically clamped onto both sidesof the chip carrier and Au electrodes were inserted through the PDMSreservoirs. The gold electrodes function as electrical connections forbiasing the PDMS chamber solutions to produce a transmembrane voltage(TMV) for driving species translocation through the nanoporeelectrophoretically.

The trans chamber was selected as the reservoir in which potentialmeasurements would be made for the nanopore sensor. Thus, the assemblywas arranged with the membrane oriented such that the nanowire waslocated facing the trans reservoir. The trans chamber was filled with asolution having a concentration of ˜10 mM buffer, with 10 mM KCl+0.1×TAEbuffer: 4 mM tris-acetate and 0.1 mM EDTA solution. The cis chamber wasaccordingly filled with a higher ionic concentration solution to providethe requisite reservoir concentration ratio to provide a higher assessresistance at the site of local potential measurement, in the transchamber. The cis chamber was filled with a solution of ˜1 M buffer, as 1M KCl+1×TAE buffer: 40 mM tris-acetate and 1 mM EDTA. Both solutionswere auto-cleaved, degassed by house vacuum and filtered by 20 nm Anotopsyringe filter (Whatman Ltd.) before use.

EXAMPLE IV Nanopore Sensing of DNA Translocation Through the Nanopore

The nanowire-nanopore structure produced by the methods of the examplesabove and assembled with the solutions having buffer concentrations asprescribed by Example III was operated for sensing translocation ofspecies objects, namely, double stranded DNA molecules of 1.4 nM pUC19(dsDNA). Both the ionic current through the nanopore and the currentfrom the nanowire FET device were measured.

The ionic current was amplified by an Axon Axopatch 200B patch-clampamplifier (Molecular Devices, Inc.) with β=0.1 (1 nA convert to 100 mV)and 2 kHz bandwidth. The nanowire FET current was amplified by a DL 1211current amplifier (DL Instruments) with a 10⁶ magnification (1 nAconvert to 1 mV) and a 0.3 ms rise time. Both the trans-membrane voltage(TMV) and voltage between the nanowire FET source and drain electrodes,V_(sd), were acquired by an Axon Digidata 1440A digitizer (MolecularDevices, Inc.). Both nanopore ionic current and nanowire FET signalswere fed into a 1440A digitizer, and recorded at 5 kHz by a computer.Operation of the nanopore sensor was carried out in a dark Faraday cage.To avoid 60 Hz noise that could be introduced by the electricalgrounding from different instruments, the ground line was removed fromall current amplifiers and all instruments (Amplifiers and digitizer)and the Faraday cage and were manually grounded to the building groundtogether.

Upon introduction of the dsDNA into the cis reservoir, intermittenttranslocation events were recorded from the nanopore ionic currentsignal channel when the TMV reached ˜2 V. For the nanowire FET signalchannel, similar events were recorded in the conductance trace withalmost perfect time correlation with the ionic current measurements.FIG. 13A is a plot, i, of the measured ionic current through thenanopore, and a plot, ii, of the measured nanowire FET conductance for a2.0 V TMV. FIG. 13B is a plot, i, of the measured ionic current throughthe nanopore, and a plot, ii, of the measured nanowire FET conductancefor a 2.4 V TMV. As the TMV was increased, the duration and frequency oftranslocation events measured by ionic current through the nanopore andmeasured by nanowire FET local potential sensing decreased and increasedrespectively. From the plots it is shown that the local potentialmeasurement sensing method perfectly tracks the sensing by conventionalionic current measurement. The local potential measurement methodthereby enables the determination of the time of and the duration oftranslocation of an object through the nanopore.

To directly compare the signal amplitudes of the FET local potentialmeasurement signal and the nanopore ionic current measurement signal,the FET conductance signal of ˜200 nS and baseline of ˜24 μS wasconverted into a current by multiplying the signal by the 150 mVsource-drain voltage. This calculation indicates that for ˜2 nA ofchange in ionic current through the nanopore, with a ˜12 nA baseline,there is produced an amplification to ˜30 nA of FET current in thenanowire local potential measurement, with a ˜3.6 μA baseline.Considering that current fabrication processes are not optimized for lownoise devices and that a far higher signal-to-noise ratio has beendemonstrated for SiNWs in general, the noise and signal-to-noise ratioof the nanowire FET itself is not be the fundamental limiting factor ofthis measurement.

EXAMPLE V Local Potential Measurement Dependence on cis and transReservoir Buffer Concentration Difference

To determine the impact of different ionic concentration fluids in thecis and trans reservoirs of the nanopore sensor, a nanowire-nanoporestructure was configured following the procedure in Example III above,but here with both cis and trans chambers filled with 1 M KCl bufferinstead of solutions having differing buffer concentrations. Operationof the nanopore sensor was then conducted with dsDNA provided in thetrans reservoir, following the procedure of Example IV above, with a TMVof 0.6 V. The ionic current through the nanopore was measured, as wasthe local potential, via nanowire FET conductance in the manner ofExample IV.

FIG. 13C provides plots of i, the measured ionic conductance and ii, themeasured FET conductance. As shown in the plots, translocation eventswere sensed by changes in ionic current when the TMV reached 0.5-0.6 Vbut the simultaneously-recorded FET conductance change was negligible atthat voltage. The reservoir solution concentration ratio is thereforeunderstood to play an important role in the signal generation.

Under the balanced buffer solution concentration conditions (1 M/1 M) ofthis experiment, the nanopore solution resistance contributes themajority of the resistance of the nanopore sensor; thus, almost all ofthe TMV drops across the nanopore. The electrical potential in thevicinity of the nanowire sensor is accordingly for this condition veryclose to ground regardless of any change in the solution resistance ofthe nanopore and access resistances of the reservoirs due to blockadeduring species translocation. Under the non-balanced buffer conditions(10 mM/1 M) of Example IV above, the nanopore solution resistance andthe trans chamber access resistance are comparable, while the accessresistance of cis chamber is still negligible. Any change of thesolution resistance in the nanopore and access resistance in the transreservoir causes a corresponding redistribution of TMV and thus a changein the electrical potential in the vicinity of the nanopore at the transchamber, and this potential change is what is easily detected by thelocal potential measurement of the nanopore sensor.

This example validates the discovery herein that local potentialmeasurement nanopore sensing requires a difference in buffer solutionconcentration between the reservoirs of a nanopore sensor, and that thelocal potential measurement is to be conducted at the reservoir-side ofthe nanopore having a higher resistance, or correspondingly lowerconcentration. This condition is not applicable to nanopore sensorswherein the membrane is sufficiently thin to operate as a nanowire andto sense the potential on both sides of the membrane, as in graphenenanopore sensors in which a graphene nanowire provides an indication ofa difference between potential on the two sides of a nanopore. In thiscase, a difference in buffer solution concentration is still preferable,but the local potential measurement is not strictly limited to one sideor the other of the nanopore, given that the nanowire measurementinherently senses the potential on both sides of the membrane.

Note in the experiments above in which the reservoir solutionconcentrations were equal and were unequal required differingtransmembrane voltages to initial translocation through the nanopore.For potential measurement in the trans reservoir, with equal solutionconcentrations, the electric field through the nanopore is constant, asshown in the plot of FIG. 3D. When the reservoir concentrations aredifferent, e.g., the 100:1 concentration of the examples above, then theelectric field through the nanopore is smaller on the cis reservoir-sideof the nanopore. To produce the same electric field as that obtainedwith equal reservoir solution concentrations, the transmembrane voltageis required to be increased by about 4 times. This explains the data ofthe plots of FIGS. 12 and 13.

EXAMPLE VI Multi-Channel Nanopore Sensing

Three nanowire nanopore sensors were constructed following the methodsof the examples above. The three nanopore sensors were integrated with acommon reservoir system, with a 1 M KCl buffer solution in the cischamber and a 10 mM KCl buffer in the trans chamber. A transmembranevoltage of 3 V was employed, and 1.4 nM of pUC19 DNA was provided fortranslocation through the nanopores.

FIG. 14 provides plots i-iv of total ionic current and the nanowire FETconductance of each of the three nanopore sensors, respectively, duringDNA nanopore translocation operation. As shown in the plots, continuoustranslocation events are observed in all three nanopore sensors as wellas the total ionic current channel. All nanopore sensors operatedindependently and every falling or rising edge apparent in the ioniccurrent channel can be uniquely correlated to a corresponding edge inone of the three nanopore sensors. Using the falling and rising edge ofsignals from all three nanopore sensors to reconstruct the total ioniccurrent trace, the reconstruction is nearly perfect for of all events.This nanopore operation demonstrates that a key advantage of thenanopore sensor is the large scale integration capability. Multipleindependent nanopore sensors can be implemented without need for complexmicro-fluidic systems.

With these examples and the preceding description, it is demonstratedthat the nanopore sensor can provide sensing of species translocatingthrough a nanopore and can discriminate between differing objects, suchas DNA bases, as those objects translocate through the nanopore. Thenanopore sensor is not limited to sensing of a particular species orclass of species and can be employed for a wide range of applications.It is recognized that the nanopore sensor is particularly well-suitedfor sensing of biopolymer molecules that are provided for translocationthrough the nanopore. Such molecules include, e.g., nucleic acid chainssuch as DNA strands, an oligonucleotide or section of single-strandedDNA, nucleotides, nucleosides, a polypeptide or protein, amino acids ingeneral, or other biological polymer chain. There is no particularlimitation to the species object to be sensed by the nanopore sensor.With differing reservoir solution concentrations, it is demonstratedthat the nanopore sensor can operate with reasonable bandwidth andsensitivity for discriminating DNA bases, and therefore enables DNAsequencing. It is recognized, that those skilled in the art may makevarious modifications and additions to the embodiments described abovewithout departing from the spirit and scope of the present contributionto the art. Accordingly, it is to be understood that the protectionsought to be afforded hereby should be deemed to extend to the subjectmatter claims and all equivalents thereof fairly within the scope of theinvention.

We claim:
 1. A multi-channel nanopore sensor comprising: a plurality ofindependent nanopore sensors; a first fluidic reservoir, common to allof the independent nanopore sensors in the plurality of independentnanopore sensors, with a first ionic solution of a first ionicconcentration disposed in the first fluidic reservoir; a second fluidicreservoir, common to all of the independent nanopore sensors in theplurality of independent nanopore sensors, with a second ionic solutionof a second ionic concentration, different than the first ionicconcentration, disposed in the second fluidic reservoir; and eachindependent nanopore sensor in the plurality of independent nanoporesensors comprising: a nanopore disposed in a support structure; afluidic connection between the first fluidic reservoir, common to all ofthe independent nanopore sensors in the plurality of independentnanopore sensors, and an inlet to the nanopore; a fluidic connectionbetween the second fluidic reservoir, common to all of the independentnanopore sensors in the plurality of independent nanopore sensors, andan outlet from the nanopore; and an electrical transduction elementdisposed in contact with that ionic solution, of the first and secondionic solutions, which has a lower ionic concentration, the electricaltransduction element being arranged at a site that produces in theelectrical transduction element an electrical signal indicative ofelectrical potential local to that ionic solution having a lower ionicconcentration.
 2. The multi-channel nanopore sensor of claim 1 whereinthe electrical transduction element of each independent nanopore sensoris disposed at one of the inlet to the nanopore and the outlet from thenanopore of that independent nanopore sensor, to indicate localelectrical potential at one of the inlet to the nanopore and the outletfrom the nanopore.
 3. The multi-channel nanopore sensor of claim 1wherein the electrical transduction element of each independent nanoporesensor comprises a plurality of electrical transduction elements, onetransduction element disposed in the first ionic solution and onetransduction element disposed in the second ionic solution, to indicatea difference in electrical potential local to the first ionic solutionand electrical potential local to the second ionic solution, between theinlet to the nanopore and the outlet from the nanopore of thatindependent nanopore sensor.
 4. The multi-channel nanopore sensor ofclaim 1 wherein the nanopore of each independent nanopore sensor has anelectrical fluidic solution resistance and the reservoir of lower ionicconcentration has an ionic concentration that provides in the reservoirof lower concentration an electrical reservoir access resistance that isof the same order of magnitude as the nanopore fluidic solutionresistance and that is at least an order of magnitude greater than areservoir access resistance of the reservoir of higher ionicconcentration.
 5. The multi-channel nanopore sensor of claim 1 whereinone of the first ionic concentration and the second ionic concentrationis at least about 20 times greater than the other ionic concentration.6. The multi-channel nanopore sensor of claim 1 wherein one of the firstionic concentration and the second ionic concentration is at least about50 times greater than the other ionic concentration.
 7. Themulti-channel nanopore sensor of claim 1 wherein one of the first ionicconcentration and the second ionic concentrations is at least about 100times greater than the other ionic concentration.
 8. The multi-channelnanopore sensor of claim 1 wherein a difference between the first ionicconcentration, of the first fluidic reservoir, and the second ionicconcentration, of the second fluidic reservoir, positions a localelectrical potential signal decay length, measured from one of the inletto the nanopore and the outlet from the nanopore of each independentnanopore sensor, that is at least about 5 nm.
 9. The multi-channelnanopore sensor of claim 1 wherein a difference between the ionicconcentration, of the first fluidic reservoir, and the second ionicconcentration, of the second fluidic reservoir, imposes a localelectrical potential signal, produced in the transduction element, thatis characterized by a bandwidth of at least about 50 MHz.
 10. Themulti-channel nanopore sensor of claim 1 wherein the nanopore of eachindependent nanopore sensor is characterized by a diameter that isbetween about 1 nm and about 5 nm.
 11. The multi-channel nanopore sensorof claim 1 wherein the nanopore of each independent nanopore sensor ischaracterized by a diameter that is between about 1 nm and about 2 nm.12. The multi-channel nanopore sensor of claim 1 wherein the electricaltransduction element of each independent nanopore sensor is disposed onthe nanopore support structure at one of the inlet to the nanopore andthe outlet from the nanopore of each independent nanopore sensor. 13.The multi-channel nanopore sensor of claim 1 wherein the electricaltransduction element of each independent nanopore sensor comprises anelectrical device or device region.
 14. The multi-channel nanoporesensor of claim 1 wherein the electrical transduction element of eachindependent nanopore sensor comprises an electrical circuit.
 15. Themulti-channel nanopore sensor of claim 1 wherein the electricaltransduction element of each independent nanopore sensor comprises atransistor.
 16. The multi-channel nanopore sensor of claim 15 whereinthe electrical transduction element of each independent nanopore sensorcomprises a field effect transistor.
 17. The multi-channel nanoporesensor of claim 16 wherein the electrical transduction element of eachindependent nanopore sensor comprises a nanowire field effecttransistor.
 18. The multi-channel nanopore sensor of claim 17 whereinthe nanowire field effect transistor of each independent nanopore sensorcomprises a silicon nanowire.
 19. The multi-channel nanopore sensor ofclaim 15 wherein the electrical transduction element of each independentnanopore sensor comprises a single electron transistor.
 20. Themulti-channel nanopore sensor of claim 15 wherein the transistor of eachindependent nanopore sensor is disposed on the nanopore supportstructure.
 21. The multi-channel nanopore sensor of claim 16 wherein thefield effect transistor of each independent nanopore sensor includes anelectronic conduction channel that is disposed at the nanopore of thatindependent nanopore sensor.
 22. The multi-channel nanopore sensor ofclaim 1 wherein the support structure in which the nanopore of eachindependent nanopore sensor is disposed comprises a membrane.
 23. Themulti-channel nanopore sensor of claim 1 wherein the support structurein which the nanopore of each independent nanopore sensor is disposedcomprises a suspended layer of graphene.
 24. The multi-channel nanoporesensor of claim 1 wherein the electrical transduction element of eachindependent nanopore sensor comprises a graphene layer in which thenanopore is disposed.
 25. The multi-channel nanopore sensor of claim 22wherein the electrical transduction element of each independent nanoporesensor comprises a nanowire disposed on the membrane at a location ofone of the inlet to the nanopore and the outlet from the nanopore ofthat independent nanopore sensor.
 26. The multi-channel nanopore sensorof claim 1 wherein the support structure of each independent nanoporesensor comprises a solid state material.
 27. The multi-channel nanoporesensor of claim 1 wherein the support structure of each independentnanopore sensor comprises a biological material.
 28. The multi-channelnanopore sensor of claim 1 wherein the support structure of eachindependent nanopore sensor comprises a lipid bilayer and wherein thetransduction element of each independent nanopore sensor comprises aregion of the lipid bilayer that includes fluorescent dye which changesfluorescence in response to changes in local electrical potential. 29.The multi-channel nanopore sensor of claim 1 wherein the nanopore ofeach independent nanopore sensor comprises a biological nanopore. 30.The multi-channel nanopore sensor of claim 1 wherein the nanopore ofeach independent nanopore sensor comprises a protein nanopore.
 31. Themulti-channel nanopore sensor of claim 1 further comprising anelectrical connection, between the first ionic solution and the secondionic solution, that applies a voltage bias between the inlet to thenanopore of each independent nanopore sensor and the outlet from thenanopore of each independent nanopore sensor to electrophoreticallydrive objects through the nanopore of each independent nanopore sensor.32. The multi-channel nanopore sensor of claim 1 wherein the electricaltransduction element of each independent nanopore sensor is arranged ata site that produces an electrical signal indicative of electricalpotential local to that ionic solution, of the first and second ionicsolutions, having a lower ionic concentration, in response to a moleculetranslocating through the nanopore of that independent nanopore sensorin the plurality of independent nanopore sensors.
 33. The multi-channelnanopore sensor of claim 1 wherein the electrical transduction elementof each independent nanopore sensor is arranged at a site that producesan electrical signal indicative of electrical potential local to thationic solution, of the first and second ionic solutions, having a lowerionic concentration, in response to translocation through the nanopore,of that independent nanopore sensor, of at least one object selectedfrom DNA, DNA fragments, RNA, RNA fragments, nucleotides, nucleosides,oligonucleotides, proteins, polypeptides, and amino acids.
 34. Themulti-channel nanopore sensor of claim 1 wherein the electricaltransduction element of each independent nanopore sensor is arranged ata site that produces an electrical signal indicative of electricalpotential local to that ionic solution, of the first ionic solution andthe second ionic solution, having a lower ionic concentration, inresponse to translocation through the nanopore of that independentnanopore sensor of a corresponding one of each of A, T, G, and C DNAbases.
 35. The multi-channel nanopore sensor of claim 31 wherein one ofthe first ionic concentration and the second ionic concentration is atleast about 100 times greater than the other ionic concentration, andfurther comprising an electrical circuit connected to the transductionelement of each independent nanopore sensor and configured to produce adifferent electrical signal for translocation of each of A, T, G, and CDNA bases through a nanopore in one of the independent nanopore sensors,with a difference of at least 5 mV between different electrical signals.36. The multi-channel nanopore sensor of claim 1 further comprisingsignal processing electronics connected to the transduction element ofeach independent nanopore sensor and configured to process indicatedelectrical potential as a function of time to determine time oftranslocation and duration of translocation of objects through thenanopore of each independent nanopore sensor in the plurality ofindependent nanopore sensors.
 37. The multi-channel nanopore sensor ofclaim 1 further comprising signal processing electronics connected tothe transduction element of each independent nanopore sensor andconfigured to process indicated electrical potential as a function oftime to identify objects as objects translocate through the nanopore ofeach independent nanopore sensor in the plurality of independentnanopore sensors.
 38. The multi-channel nanopore sensor of claim 1further comprising signal processing electronics connected to thetransduction element of each independent nanopore sensor configured toprocess indicated electrical potential as a function of time to identifyDNA bases as DNA bases translocate through the nanopore of eachindependent nanopore sensor in the plurality of independent nanoporesensors.
 39. A multi-channel nanopore sensor comprising: a plurality ofindependent nanopore sensors; a first fluidic reservoir, common to allof the independent nanopore sensors in the plurality of independentnanopore sensors, with a first ionic solution of a first ionicconcentration disposed in the first fluidic reservoir; a second fluidicreservoir, common to all of the independent nanopore sensors in theplurality of independent nanopore sensors, with a second ionic solutionof a second ionic concentration, different than the first ionicconcentration, disposed in the second fluidic reservoir; and eachindependent nanopore sensor in the plurality of independent nanoporesensors comprising: a biological nanopore; a fluidic connection betweenthe first fluidic reservoir, common to all of the independent nanoporesensors in the plurality of independent nanopore sensors, and an inletto the biological nanopore; a fluidic connection between the secondfluidic reservoir, common to all of the independent nanopore sensors inthe plurality of independent nanopore sensors, and an outlet from thebiological nanopore; and an electrical transduction element disposed incontact with that ionic solution, of the first and second ionicsolutions, which has a lower ionic concentration, the electricaltransduction element being arranged at a site that produces in theelectrical transduction element an electrical signal indicative ofelectrical potential local to that ionic solution having a lower ionicconcentration.